asta j pro ect patient specific modeling of abdominal ... · abdominal aortic aneurysms(aaas) ......

ASTA jPatient‐Specific Modeling of

ASTA project

Abdominal Aortic Aneurysms(AAAs)Anirban Jana, PhDAnirban Jana, PhDProf Ender FinolO t b 17 2011

© 2011 Pittsburgh Supercomputing Center

October 17, 2011

Motivation and broad objectives Increase in diameter of more than 50% (normal

healthy diameter of ~2 cm)

Present in as many as 8.8% of the population over the age of 65the age of 65

AAA rupture 10th leading cause of death for men above the age of 50

l l f Current protocol – surgical repair if maximum AAA diameter > 5 ‐ 6 cm or growth rate > 1 cm/yr. But often smaller AAAs rupture, while larger ones do not

Risk of rupture vs Risk of surgical intervention Risk of rupture vs Risk of surgical intervention

Biomechanical assessment for rupture potential

Aorta

Renal Arteries p p

Influence of variations in individual biomechanical variablesRight common

iliac artery

© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol

Left common iliac artery

AAA researchBiomechanicsComputational modeling techniques

• Fillinger, M.F., Raghavan, M.L., Marra S.P., Cronenwett, J.L., Kennedy, F.E., Journal of Vascular Surgery 33(3):589‐597 (2002). • Di Martino E.S., Gudagni, G., Fumero, A., Ballerini, G. Spirito R., Biglioli, P., Redaeilli A., Medical Engineering Physics 23(9):647‐655 (2001).• Scotti C.M., Shkolnik, A.D., Muluk, S., Finol, E.A., Biomed Engineering Online 4:64 (2005).

• Di Martino E.S., Gudagni, G., Fumero, A., Ballerini, G. Spirito R., Biglioli, P., Redaeilli A., Medical Engineering Physics 23(9):647‐655 (2001).• Olufsen, M.S., Peskin, C.S., Kim, W.Y., Pedersen, E.M., Nadim, A., Larse, J., Annals of Biomedical Engineering, 28:1281‐1299 (2000). • Steele, B.N., Taylor, C.A., Proceedings of the 2003 ASME Summer Bioengineering Meeting (2003). Vi Cl t l I E Fi C A J K E T l C A C t th d A l M h E 195 3776 3796 (2006)

Boundary conditions

• Vignon‐Clementel , I.E., Figueroa C.A., Jansen K.E., Taylor, C.A, Computer methods Appl. Mech. Eng. 195:3776‐3796 (2006).• Scotti, C.M., Jimenez, J., Muluk, S.C., Finol, E.A., Computer methods in Biomechanics and Biomedical Engineering 11(3):301‐322 (2008).

Material models/properties• Di Martino, E., Mantero, S., Inzoli, F., Melissano, G., Astore, D., Chiesa, R., Fumero, R, European Journal of Vascular Endovascular Surgery

Mesh generation

15:290‐299 (1998).• Raghavan, M.L., Webster, M.W., Vorp, D.A., Journal of Biomechanics, 33:475‐482 (2000). • Vande Geest , J.P.,Sacks, M.S., Vorp, D.A., Journal of Biomechanics, 39(7):1324‐1334 (2006).• Vande Geest, J.P. ,Sacks, M., Vorp, D.A., Journal of Biomechanics, 39, 2347‐2354 (2006)

Mesh generation• Wolters, B. J., Rutten, M. C., Schurink, G. W., Kose, U., de Hart, J., and van de Vosse, F. N., 2005, Med Eng Phys, 27(10), pp. 871‐883.• Auer M, G. T., 2010, IEEE Trans Med Imaging, pp. 1022‐1028.• Zhang,Y., Wang,W., Liang, X., Bazilevs,Y., Hsu,M.‐C.,Kvamsdal,T.,Brekken,R., Isaksen, J., 2009, CMES Comp Mod in Eng and Sc, 42(2), pp. 1‐18.• Shim, M.‐B., Gunay, M., and Shimada, K., 2009, Computer‐Aided Design, 41(8), pp. 555 ‐ 565.Sh J X A Ch t t h I Fi l E A 2011 A l f Bi di l E i i 39(1) 249 259


Pathogenesis Genetics Molecular biology Medical imaging• Shum, J., Xu, A., Chatnuntawech, I., Finol, E. A., 2011, Annals of Biomedical Engineering, 39(1), pp. 249‐259.

Model constructionM di l i b d ti t ifi d liMedical image based patient specific modeling

CT/MRIimage

Segmentation inVESSEG

2D masks 3D reconstructed geometry/surface mesh

Volume mesh

Wall Computational predictions

Thrombus

Lumen

predictions (stress, strain etc)


SoftwarePreprocessing (model construction boundary conditions)Preprocessing (model construction, boundary conditions)

MATLABwww.mathworks.com

Biomechanics simulations (CFD CSS and FSI)Biomechanics simulations (CFD, CSS and FSI)ADINA (a commercial finite‐element multiphysics package;

developed by Prof K.J.Bathe, Mech Eng, MIT)

Post‐processing

www.adina.com

ENSIGHT, MATLABPost processing

www.ensight.com


www.ensight.com

My contributionsHelp improve TeraGrid/XSEDE research proposals (benchmarkingHelp improve TeraGrid/XSEDE research proposals (benchmarking, scaling, SU justification)

Provide guidance and troubleshooting advice for ADINA (choosingProvide guidance and troubleshooting advice for ADINA (choosing best ADINA simulation options and element types, output control)

Provide expert advice on efficient MATLAB coding

Develop patient specific boundary conditions (MATLAB codes)

Provide expertise in computational fluid dynamics and computational solid mechanics on a reg lar basis to enhance science o tp tsolid mechanics on a regular basis to enhance science output

Co‐author papers, critique manuscripts and presentation slides


Co author papers, critique manuscripts and presentation slides

My contributionsPublications1) S. Raut, S. Chandra, A. Jana and E. Finol, Individual Anisotropic FSI Modeling of Aortic Aneurysms: Phase Contrast and

Dynamic MRI validation, 2009 Biomedical Engineering Society Annual Fall Meeting, Pittsburgh, PA, October 2009 (Peer reviewed poster presentation).

2) S. Raut, S. Chandra, A. Jana, S. Muluk and E. Finol, The Effect of Local Infrarenal Flow Conditions on Intra‐aneurysmalFlow Dynamics, 2009 Biomedical Engineering Society Annual Fall Meeting, Pittsburgh, PA, October 2009 (Peer reviewed poster presentation).

3) Samarth S. Raut, Anirban Jana, Ender A. Finol, Effects Of Shape Versus Material Model Variations On AAA Wall Mechanics, Sixth M.I.T. Conference on Computational Fluid and Solid Mechanics, Boston, MA, June 2011 (Peer‐reviewed abstract and presentation)abstract and presentation).

4) Samarth Raut, Peng Liu, Anirban Jana, Ender Finol, Aortic Wall Mechanics: A Geometry‐Driven Problem, ASME 2011 Summer Bioengineering Conference, Farmington, PA, June 2011 (Peer‐reviewed abstract and poster).

5) Samarth Raut, Judy Shum, Santanu Chandra, Anirban Jana, Peng Liu, Kibaek Lee, Elena Di Martino, Todd Doehring, Ender Finol, AAAVASC: A novel Integrated Approach for Image Based Modeling Toward Individualized AAA Rupture RiskEnder Finol, AAAVASC: A novel Integrated Approach for Image Based Modeling Toward Individualized AAA Rupture Risk Assessment,2011 Biomedical Engineering Society Annual Meeting, Hartford, CT, October 2011 (Peer‐reviewed abstract and presentation).

MentoringAdvisory Committee and Co‐advisor, Samarth Raut, PhD candidate, Mechanical Engineering, Carnegie Mellon University, Biomechanics of Abdominal Aortic Aneurysms.


AAA parallel simulation benchmarks14000

Performed previously on PSC’s Pople, currently on PSC’s Blacklight

Computational Solid Stress (CSS) 12000

14000

simulation of a patient AAA wall 2,889,837 degrees of freedom Memory required ~13 GB

8000

10000

tatio

nal tim

e,s

ADINA SMP version 8 cores optimal for this problem, up to

32 cores if fastest time to solution desired (for this problem size)

4000

6000

Compu

t

desired (for this problem size)

0

2000

0 10 20 30 40 50 60##cores


CSS validation for hyperelastic materials0

8 9 10 11 12 13 14l Element type

6

‐4

‐2

8 9 10 11 12 13 14

ror in max prin

cipa

lstress

Hex20

Hex8

Pri15

Tet11

Element type

Straight tube section, plain strain,i ibl M Ri li t i l

‐8

‐6

% err

ln( # of Equations )

Tet11

Hex27

8incompressible Mooney‐Rivlin material

Analytical solution12

4

6

n(Time)

Hex27

Hex20

Hex8

P i15

‐4

‐2

00 2 4 6 8 10 12 14

ln

ln(#Eqns)

Pri15

Tet11

Tet11most efficient, followed by Hex27, but Pri15 also not too bad ILT ‐> Tet11, wall‐> Hex27 or Pri15


1 Batra R. C. , ‘Finite plane strain deformation of rubberlike materials’ , Int. J Num Method in Eng, vol.15, 145‐160,1980

CSS validation for hyperelastic materialsAdditional observations

3D iterative solver fails to converge for all element types except Tet11. Sparse solver converges for almost all cases. However, sparse solver consumes more memory and time

Additional observations

converges for almost all cases. However, sparse solver consumes more memory and time compared to 3D iterative solver (up to 2x, especially for large models).

ADINA cannot simulate perfectly incompressible (Poisson’s ratio =0.5)Mooney‐Rivlinmaterials, but can model almost incompressible Mooney‐Rivlin materials (Poisson’s ratio =0.49, 0.499, …). We tested the sensitivity of the results as the Poisson’s ratio is made to , , ) yapproach the limiting value of 0.5.


Geometry reconstruction and meshing AAAVASC : A unified framework for multi‐domain mesh generation from medical images

Written in MATLABWritten in MATLAB

Surface meshes generated first, followed by volume meshes

Completely unstructured meshes for ILT and lumen, extruded mesh for wall (based on prescribed uniform/non‐uniform thickness)

Smoothing operations performed to reduce mesh irregularities and improve element quality

Computes some geometric parameters of the final model, e.g., volume, surface area, curvatures


Boundary conditionsPlug profile

• Circle fit to convex hull of inlet surface mesh

Parabolic profile• Circle fit to convex hull of inlet surface mesh• Hagen Poiseuille eqn for velocity profile (u (t)=2 u (t) )

Flow rate waveform

• Hagen‐Poiseuille eqn for velocity profile (umax(t)=2 uavg(t) )

Womersley profileCi l fi h ll f i l f h• Circle fit to convex hull of inlet surface mesh

• Fourier decomposition of flow rate waveform• Womersley eqn of velocity profile at specific frequencies

Patient specific profile• Schwarz‐Christoffel mapping of phase‐contrast MR image to inlet mesh


Boundary conditions

•Differences between computationally predicted average velocity and pressure at midsection and MR measured flow rate at midsection was recorded to be the greatest for the inlet plug profile

• Comparison of FSI predicted stress was also performed with patient specific vs Womersley profile prescribed at inlet

• Both amplitude and phase errors were observed for the WomersleyBoth amplitude and phase errors were observed for the Womersleyprofile


Concluding remarks B d h l M di l i b d i l i f Broad research goal: Medical image based simulation of biomechanical response of AAAs, towards AAA rupture risk prediction

My activities: Proposal writing, parallel benchmarking, simulation y p g, p g,software (ADINA) options and troubleshooting, MATLAB coding, advising student research, publications/presentations

R h t hi h I t ib t d b d diti h Research areas to which I contributed: boundary conditions, mesh generation, AAA biomechanics simulation strategies and algorithms


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